Calculate the mass defect of a molecule without empirical mass

Hello,
I'm currently writing a chemistry program. The user can create any kind of atom he can imagine, and then combine them into molecules. To properly calculate all the energies involved I need a formula to calculate the mass defect of a nucleus. I mustn't use empirical data to allow for theoretically possible, but not yet observed atoms, like some higher magic number ones.

Having said that, I am not a physicist, I'm a chemist, and my knowledge of quantum physics is meager to say the least. So here's what I tried, but it might just be rubbish for all I know :

- I started of with the theory, that due to the small mass of the electrons, only the forces within the nucleus play any significant part in the mass defect.

- But if I were to include electrons, they would be affected by gravity(between each other and the nucleus) and coloumb forces (between each other and the protons in the nucleus). Additionally I think I once read that due to the electrons being charged moving particles, a magnetic field is being created, that resonates with the nucleus. I do not understand it, so for now I concluded that it's irrelevant for the mass defect even compared to the other "irrelevant" forces.

- The forces within the nucleus are primarily the strong and weak forces. These are what mainly causes the mass defect. Weak Forces only work "on direct contact", which is the reason why larger atoms become instable. The Strong Force can be calculated, as is described here ( http://physics.stackexchange.com/questions/8452/is-there-an-equation-for-the-strong-nuclear-force ), but I do not understand how I could remodel the equation to work on entire nuclei. The Weak Forces seem to be a mystery .

I also tried to calculate the interactions based on their wave functions, but even early tests turned out to be extremely processor intensive, so I concluded that this was not a valid path to go.

Are these assumptions all correct?
And is there any way to accurately (significantly) calculate the mass defect in theoretical atoms? Or do things like the Three-body-problem make it all together impossible?

If it is possible, I'd really appreciate any help you can give me.
Thanks!

At these small scales, I think you are over-estimating the effect plain old gravity has on elementary particles. I believe gravity is the weakest force at these scales, followed by the weak nuclear force, the Coulomb (electromagnetic)force, and then the strong nuclear force, in that order.

I applaud what you are trying to do, but you should be cognizant of the fact that theoretical physicists who have a more intimate knowledge of atomic structure and the forces present have struggled to do what you are attempting.